26 October 2017
R to visualize your data
Why visualize your data?
- summarize information
- check assumptions validity
- many pieces of information at one glance
- ease the understanding
Why use R to do it?
Workflow
    Â
Why use R to do it?
Workflow
     Â
Why use R to do it?
Here we'll argue why use R for doing your plots:
- visualizing data
- what makes a good graph (some details)
- work-flow (data are already in R)
- base graph / ggplot2 / web graphs (interacting)
- code / reproducible
Why use R to do it?
Many ways to visualize
Why use R to do it?
Many, many, many packages available
Why use R to do it?
Why use R to do it?
Few lines of codes
library(raster)
library(mapview)
elvBtn = getData('alt', country='BTN', path='./assets/')
mapview(elvBtn)
Why use R to do it?
Few lines of codes
Why use R to do it?
A large community
Why use R to do it?
Common plots used in meta-analyses with R
What do we want/need to visualize?
Effect size
- log risk ratios,
- log odds ratios,
- mean differences,
- standardized mean differences,
- …
Number of study
- by author
- by region
- by species
Effect size – Funnel plot
Effect size – Radial plot
Effect size – Forest plot
Vellend et. al 2013
Effect size – Forest plot
Number of Study & effect size
Vellend et al. 2013
Number of Study & geography
Vellend et al. 2013
R packages for meta-analyses
install.packages("ctv"); ctv::install.views("MetaAnalysis")
Meta vs Metafor – support
Guido Schwarzer author of
metaSchwarzer, Guido, James R. Carpenter, and Gerta Rücker. Meta-Analysis with R.
Wolfgang Viechtbauer author
metafor
Meta vs Metafor – workflow
meta:
metafor:
So…
Everything you need is online
A problem… just google it!
How can we help you?
Install packages
install.packages('metafor')
library('metafor')
rma()
?rma
Funnel plot
Funnel plot
Funnel plot – version 2
Funnel plot – version 3
Forest plot
Custom your plot
Few tips
Few tips
- Axis
- Legend
- points
- lines
- colors
- text
Questions?
Let's practice
Reproduce 2 figures from Vellend et al. 2013
Data available on line as well Dataset S1
Figure 3
Figure S2
Vellend et al. 2013
Let's have some fun
WordCloud
library(wordcloud2) wordcloud2(demoFreq) wordcloud2(demoFreq, size = 2)
https://github.com/inSileco/wordcloud/blob/master/ourWordcloud.R
WordCloud
Network of co-authors
igraph
Resources
Useful links
2 books:
Chen, Ding-Geng, and Karl E. Peace. Applied Meta-Analysis with R. Chapman & Hall/CRC Biostatistics Series. Boca Raton: CRC Press/Taylor & Francis Group, 2013. + companion website
Schwarzer, Guido, James R. Carpenter, and Gerta Rücker. Meta-Analysis with R. Use R! Cham: Springer International Publishing, 2015. https://doi.org/10.1007/978-3-319-21416-0.